Protonation function input error

[Xinchunran]

For the 5FLM.pdb, the RNA polymerase, which contains the nucleotide U. The pdb structure parser will recognize the U as a metal ion in the ligand

import enzy_htp.structure as struct
import enzy_htp.structure.structure_operation as stru_oper
from enzy_htp.preparation import protonate as prot

sp = struct.PDBParser()

def test_protonate(test_pdb:str):
    stru = sp.get_structure(test_pdb)
    prot.protonate_stru(stru, 7.0, protonate_ligand=True)

def args():
    pass

def main():
    pdb_list = ["5FLM.pdb", "1F6G.pdb"]
    for pdbs in pdb_list:
        test_protonate(f"../{pdbs}")
        print("finish {pdbs}")

if __name__ == "__main__":
    main()